Human endogenous retrovirus onco-exaptation counters cancer cell senescence through calbindin
Jan Attig, … , Charles Swanton, George Kassiotis
Jan Attig, … , Charles Swanton, George Kassiotis
Published May 16, 2023
Citation Information: J Clin Invest. 2023;133(14):e164397. https://doi.org/10.1172/JCI164397.
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Human endogenous retrovirus onco-exaptation counters cancer cell senescence through calbindin

Abstract

Increased levels and diversity of human endogenous retrovirus (HERV) transcription characterize most cancer types and are linked with disease outcomes. However, the underlying processes are incompletely understood. Here, we show that elevated transcription of HERVH proviruses predicted survival of lung squamous cell carcinoma (LUSC) and identified an isoform of CALB1, encoding calbindin, ectopically driven by an upstream HERVH provirus under the control of KLF5, as the mediator of this effect. HERVH-CALB1 expression was initiated in preinvasive lesions and associated with their progression. Calbindin loss in LUSC cell lines impaired in vitro and in vivo growth and triggered senescence, consistent with a protumor effect. However, calbindin also directly controlled the senescence-associated secretory phenotype (SASP), marked by secretion of CXCL8 and other neutrophil chemoattractants. In established carcinomas, CALB1-negative cancer cells became the dominant source of CXCL8, correlating with neutrophil infiltration and worse prognosis. Thus, HERVH-CALB1 expression in LUSC may display antagonistic pleiotropy, whereby the benefits of escaping senescence early during cancer initiation and clonal competition were offset by the prevention of SASP and protumor inflammation at later stages.

Authors

Jan Attig, Judith Pape, Laura Doglio, Anastasiya Kazachenka, Eleonora Ottina, George R. Young, Katey S.S. Enfield, Iker Valle Aramburu, Kevin W. Ng, Nikhil Faulkner, William Bolland, Venizelos Papayannopoulos, Charles Swanton, George Kassiotis

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Figure 3

KLF5-regulated HERVH-CALB1 activity marks squamous cell differentiation.

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KLF5-regulated HERVH-CALB1 activity marks squamous cell differentiation....
(A) Hierarchical clustering of HERVH-CALB1–positive and –negative TCGA LUSC samples (P = 362) according to differential expression (≥2-fold, q < 0.05) of 1,526 genes (left). PTEN mutation status and SOX2 expression are also indicated. Functional annotation by gene ontology (GO) of the 1,133 genes (boxed) upregulated in HERVH-CALB1–positive samples (right). P values calculated with the g:SCS algorithm. (B) Hematoxylin and p63 immunostaining of liver sections from Rag2–/–Il2rg–/–Cd47–/– recipients of LK-2 or LK-2 2B7 cells. Left, 2 representative mice from each group. Scale bars: 50 μm. Percentage of p63+ cells in LK-2 and LK-2 2B7 tumors in the same mice (right). Symbols represent individual mice with 3 regions per mouse. P value calculated with Mann-Whitney rank-sum test. (C) Spearman’s rank correlation of HERVH-CALB1 and transcription factor expression in TCGA LUSC RNA-Seq data. (D) Percentage change in HERVH LTR7-GFP reporter activity in transcription factor–transfected HEK293T.LTR7-GFP cells, compared with untransfected HEK293T.LTR7-GFP cells. Symbols represent separate transfections. P values calculated with paired Student’s t test. (E) Annotated CALB1 gene and HERVH provirus, HERVH-CALB1 transcript, KFL5 peaks in ChIP-Seq data from HARA cells (GSE147853), and RNA-Seq traces of HARA cells and KFL5-deficient HARA cells (HARA.KLF5–/–) (GSE147855). (F) HERVH-CALB1 expression in HARA and HARA.KLF5–/– cells in E. Symbols represent experimental replicates. P value calculated with Student’s t test. (G) Enrichment in KLF5 binding to LTR7Y and LTR7 HERVH LTRs, present in full-length proviruses or as solitary (solo) LTRs, in HARA cell ChIP-Seq data (GSE147853). (H) HERVH proviruses differentially expressed between HARA and HARA.KLF5–/– cells (GSE147855), ranked by PCA component 1 and annotated according to LTR type. (I) Expression of HERVH-CALB1 determined by RT-qPCR in KLF4- or KLF5-transfected LK-2 and NCI-H2170 cells, compared with untransfected respective cells. Error bars represent the variation of 3 independent repeats. P values were calculated with Student’s t tests.